Problem with large /etc/passwd

I have found a problem with ISPconfig server. It has corrupted the /etc/passwd during the update process.
It has happen several times, only which server has large number of users. The server has more then 3000 user under single domain. I am running 3 more ISPconfig server, which has many domains but with few email users are working very nice.

Is it possible to stop the auto update of /etc/passwd . I want run the update command manualy when the server is free.